FPGA-based data acquisition and processing systems play an important role in modern high-speed, multichannel measurement systems, especially in High-Energy and Plasma Physics. Such FPGA-based systems require an extended control and diagnostics part corresponding to the complexity of the controlled system. Managing the complex structure of registers while keeping the tight coupling between hardware and software is a tedious and potentially error-prone process. Various existing solutions aimed at helping that task do not perfectly match all specific requirements of that application area. The paper presents a new solution based on the XML system description, facilitating the automated generation of the control system’s HDL code and software components and enabling easy integration with the control software. The emphasis is put on reusability, ease of maintenance in case of system modification, easy detection of mistakes, and the possibility of use in modern FPGAs. The presented system has been successfully used in data acquisition and preprocessing projects in High-Energy Physics experiments. It enables easy creation and modification of the control system definition and convenient access to the control and diagnostic blocks. The presented system is an open-source solution and may be adopted by the user for particular needs.